Locus 943

Sequence ID	3L_DroMel_CAF1
Location	2,829,383 – 2,829,483
Length	100
Max. P	0.848460

overview

Window 1

Location	2,829,383 – 2,829,483
Length	100
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	79.77
Mean single sequence MFE	-25.15
Consensus MFE	-12.80
Energy contribution	-12.47
Covariance contribution	-0.33
Combinations/Pair	1.25
Mean z-score	-2.52
Structure conservation index	0.51
SVM decision value	0.78
SVM RNA-class probability	0.848460
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2829383 100 + 23771897
AAGCACG---CACACAAAUACACAAGAAAUUAACGAGCAAACGAUUUUUAUGGCAGUAUUUUGUGCCUUAAAGCGCUUAAUGCGAUUUAUGU----------------UUGUGUGCGUU
....(((---((((((((((..(((((((((...........))))))).))...(((((..((((......))))..)))))......)))----------------)))))))))). ( -29.30)
>DroGri_CAF1 89154 97 + 1
AAAA------AAAACAAGUACACAAGAAAUUAACGAGCAAACAAUUUUUAUGGCAGCAUUUUGUGCCUUAAAGCGCUUAAUGCGCUUUAUGG------CUAUAUAU----------AGA
....------...(((((....(((((((((...........))))))).)).......)))))(((.((((((((.....)))))))).))------).......----------... ( -19.50)
>DroSec_CAF1 74398 100 + 1
AAGCACG---CACACAAAUACACAAGAAAUUAACGAGCAAACGAUUUUUAUUGCAGUAUUUUGUGCCUUAAAGCGCUUAAUGCGAUUUAUGU----------------UUGUGUGCGUU
....(((---((((((((((................((((..........)))).(((((..((((......))))..)))))......)))----------------)))))))))). ( -30.60)
>DroWil_CAF1 66836 119 + 1
AAAUACAAAAAACACAAGUAUACAAGAAAUUAACGAGCAGACGAUUUUUAUGGCAGCAUUUUGUGCCUUAAAGCGCUUAAUGUGUUUUAUACAUACAUACAUGCAUAUUAAUAUGAGAA
................(((((.(((((((((..(.....)..))))))).))...((((..((((...((((((((.....))))))))....))))...))))))))).......... ( -16.30)
>DroYak_CAF1 77392 100 + 1
AAGCACG---CACACAAAUACACAAGAAAUUAACGAGCAAACGAUUUUUAUGGCAGUAUUUUGUGCCUUAAAGCGCUUAAUGCGAUUUAUGU----------------UUGUGUGCGUU
....(((---((((((((((..(((((((((...........))))))).))...(((((..((((......))))..)))))......)))----------------)))))))))). ( -29.30)
>DroAna_CAF1 62780 98 + 1
AAACACG---CACACAAGUACACAAGAAAUUAACGAGCAAACGAUUUUUAUGGCAGCAUUUUGUGCCUUAAAGCGCUUAAUGCGAUUUAUGU----------------GAGUGUG--UU
.((((((---(.((((......(((((((((...........))))))).))...(((((..((((......))))..)))))......)))----------------).)))))--)) ( -25.90)
>consensus
AAACACG___CACACAAAUACACAAGAAAUUAACGAGCAAACGAUUUUUAUGGCAGCAUUUUGUGCCUUAAAGCGCUUAAUGCGAUUUAUGU________________UUGUGUGCGUU
..((((..................(((((((...........)))))))......(((((..((((......))))..)))))...........................))))..... (-12.80 = -12.47 +  -0.33)

alignment

secondary structure

dotplot

Window 2

Location	2,829,383 – 2,829,483
Length	100
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	79.77
Mean single sequence MFE	-24.51
Consensus MFE	-10.49
Energy contribution	-10.82
Covariance contribution	0.34
Combinations/Pair	1.17
Mean z-score	-2.54
Structure conservation index	0.43
SVM decision value	0.21
SVM RNA-class probability	0.635538
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2829383 100 - 23771897
AACGCACACAA----------------ACAUAAAUCGCAUUAAGCGCUUUAAGGCACAAAAUACUGCCAUAAAAAUCGUUUGCUCGUUAAUUUCUUGUGUAUUUGUGUG---CGUGCUU
.((((((((((----------------((((((..(((.....))).((((.((((........)))).)))).....................))))))..)))))))---))).... ( -27.70)
>DroGri_CAF1 89154 97 - 1
UCU----------AUAUAUAG------CCAUAAAGCGCAUUAAGCGCUUUAAGGCACAAAAUGCUGCCAUAAAAAUUGUUUGCUCGUUAAUUUCUUGUGUACUUGUUUU------UUUU
...----------.......(------((.((((((((.....)))))))).)))............(((((((((((.........)))))).)))))..........------.... ( -20.70)
>DroSec_CAF1 74398 100 - 1
AACGCACACAA----------------ACAUAAAUCGCAUUAAGCGCUUUAAGGCACAAAAUACUGCAAUAAAAAUCGUUUGCUCGUUAAUUUCUUGUGUAUUUGUGUG---CGUGCUU
.((((((((((----------------((.((((.(((.....))).)))).)((((((...((.((((..........))))..)).......)))))).))))))))---))).... ( -27.80)
>DroWil_CAF1 66836 119 - 1
UUCUCAUAUUAAUAUGCAUGUAUGUAUGUAUAAAACACAUUAAGCGCUUUAAGGCACAAAAUGCUGCCAUAAAAAUCGUCUGCUCGUUAAUUUCUUGUAUACUUGUGUUUUUUGUAUUU
............((((((((....))))))))....(((..((((((((((.((((........)))).))))....((.(((.............))).))..))))))..))).... ( -20.52)
>DroYak_CAF1 77392 100 - 1
AACGCACACAA----------------ACAUAAAUCGCAUUAAGCGCUUUAAGGCACAAAAUACUGCCAUAAAAAUCGUUUGCUCGUUAAUUUCUUGUGUAUUUGUGUG---CGUGCUU
.((((((((((----------------((((((..(((.....))).((((.((((........)))).)))).....................))))))..)))))))---))).... ( -27.70)
>DroAna_CAF1 62780 98 - 1
AA--CACACUC----------------ACAUAAAUCGCAUUAAGCGCUUUAAGGCACAAAAUGCUGCCAUAAAAAUCGUUUGCUCGUUAAUUUCUUGUGUACUUGUGUG---CGUGUUU
..--.((((.(----------------((((((..((((.((((((.((((.((((........)))).))))...)))))).............))))...)))))))---.)))).. ( -22.64)
>consensus
AACGCACACAA________________ACAUAAAUCGCAUUAAGCGCUUUAAGGCACAAAAUACUGCCAUAAAAAUCGUUUGCUCGUUAAUUUCUUGUGUACUUGUGUG___CGUGCUU
...........................((((((..((((.((((((.((((.((((........)))).))))...)))))).............))))...))))))........... (-10.49 = -10.82 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:02 2006